Extending assembly of short DNA sequences to handle error
Extending assembly of short DNA sequences to handle error
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DOI：
10.1093/bioinformatics/btm451
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发表时间：
2007-11-01
期刊：
影响因子：
5.8
通讯作者：
Jones, Corbin D.
中科院分区：
文献类型：
--
作者：
Jeck, William R.;Reinhardt, Josephine A.;Jones, Corbin D.
现在可以使用几种新的测序技术来实现廉价的从头基因组测序，特别是在具有小基因组的生物中。其中一些技术（例如来自Illuminas solexa测序）通过产生大量的小读数（类似于30 bp）来产生高基因组覆盖范围。虽然先前的工作表明，部分组装可以通过K-MER扩展在无错误的读取中执行，但该算法对实践中的测序错误率没有成功。我们提出VCAKE（通过K-MER扩展通过验证的共识组装），这是对简单的K-Mer扩展的修改，该扩展通过使用高深度覆盖范围来克服误差。尽管这是对先前方法的简单修改，但我们在包括错误的模拟和实验数据集上显示了汇编结果的显着改善。
Inexpensive de novo genome sequencing, particularly in organisms with small genomes, is now possible using several new sequencing technologies. Some of these technologies such as that from Illuminas Solexa Sequencing, produce high genomic coverage by generating a very large number of small reads (similar to 30 bp). While prior work shows that partial assembly can be performed by k-mer extension in error-free reads, this algorithm is unsuccessful with the sequencing error rates found in practice. We present VCAKE (Verified Consensus Assembly by K-mer Extension), a modification of simple k-mer extension that overcomes error by using high depth coverage. Though it is a simple modification of a previous approach, we show significant improvements in assembly results on simulated and experimental datasets that include error.